* added new module snpsift/split
* added options.args
* added .vcf.gz to input
* removed test and updated to new NF DSL2 syntax
* Updated to new NF DSL2 syntax
* added option to join vcf files
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
* committing to pull updated nf-core files
* saving changes to checout other branch
* committing progress so far, difficulty with test data
* uploading to be used as draft PR
* fix linting error in meta.yml
* attempt to group reference inputs together
* updated input format for resources
* meta.yml updated with new resource names
* added output channel for recal index
* module only takes single vcf file input now
* committing to checkout
* update to new syntax, remove indel test for now
* updated to use memory options and new test data
* Update modules/gatk4/variantrecalibrator/main.nf
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
* Update main.nf
* Update modules/gatk4/variantrecalibrator/main.nf
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
* remove duplicate test keys from test_data.config
Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
* initial commit to setup branch
* workflow finished
* Update nextflow.config
* tumour to tumor, getpileup passed as nomral and tumor
* paired_somatic renamed to tumor_normal_somatic
* Apply suggestions from code review
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* Update subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/main.nf
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* updated index names in meta.yml
* changed index file names in main script and test
* Apply suggestions from code review
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* Apply suggestions from code review
* fixed bug from changes
* Apply suggestions from code review
* modified yml to allow new subworkflow testing
* Update test.yml
* Update test.yml
* add applyvqsr
* added memory options, new test data used
* Update main.nf
* Update main.nf
Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* Initial structure
* Working with local singularity image
* Working generateMap.pl script
* Remote not working bioconda
* Working generateMap with biocontainer
* Lint changes
* Updated hmmcopy container version to be consistent
* Fix failing test
* Remove path to perl
* No hardpath to script
* Update main.nf
Moved version outside of process, add support for zipped fasta file
* Revert to not allowing gzip via pipe, as perl script can't cope
Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk>
* initial commit to setup branch
* workflow finished
* Update nextflow.config
* tumour to tumor, getpileup passed as nomral and tumor
* paired_somatic renamed to tumor_normal_somatic
* Apply suggestions from code review
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* Update subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/main.nf
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* updated index names in meta.yml
* changed index file names in main script and test
* Apply suggestions from code review
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* Apply suggestions from code review
* fixed bug from changes
* Apply suggestions from code review
* modified yml to allow new subworkflow testing
* Update test.yml
* Update test.yml
* added output channel for tbi files, tweaked method of adding blank inputs for gendb tests
* Update main.nf
* Update main.nf
Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* feat: each output type has dedicated channel replace bgzip with gzip can only zip one at a time
* Add condition moving of unbinned files
* fix: solution for moving sometimes non-existant files
* fix: update meta.yml to add the new channels
* fix: remove most of the checksums due to variability
* fix: tweaking of output
* Update modules/metabat2/metabat2/main.nf
Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
* Fix find commands
* Fix find commands
Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
* added code for subworkflow fgbio call umi consensus
* ironing out a few typos etc
* fixing last things
* fixed md5sum - lets see if it changes
* removing file accidentally deleted
* tidy indents
* added bwamem2 alternative
* fixed entry for both tests
* changed name second test workflow entry
* fixed workflow entry names
* fixed md5sum for file generated with bwamem2
* added syntax new DSL2
* added new config location in test command line
* added new config location in test command line
* use of prefix instead of suffix because modules have been changed in this way
* explicit alias to bwa mem1 to avoid confusion
* removed param that should be an ext optional argument in fgbio groupreadsbyumi
* missing colon in config
* missing colon in module config too
* order list alphabetically
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* remove params from body
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* improving readability of input structure
Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
* reverting to mandatory input
* fixed tests and workflow take values
* remove param
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* simplify tests params
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* formatting inputs for readability
* factoring in changes to bwamem2_mem and bwa_mem sort/view inputs
* updating test md5sum for grouped file following code update in bwamem
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
* feat: view is now in args2 so we can use sort
* forgot one split_cpus
* feat: update with new logic
* fix: add more info
* fix: remove split_cpus logic
* greatly simplify syntax
* feat: add subworkflows to annotate (+ bgzip/tabix index) with ensemblvep and snpeff
* feat: get versions from all tools
* add commented infor for new annotation modules
* Add comment line for consistency
* Remove all functions.nf
* Remove include functions.nf and publishDir options
* Replace options.args3 with task.ext.args3 - 3 modules
* Replace options.args3 with task.ext.args3 - 17 modules
* Replace {task.cpus} with task.cpus
* Replace off on off off off off off off off on off on off on off off off on off off off on on off off off on on off off off off off off off on off off off off on off on on off off off on on on on off off off on off on on off on on off off on on on off on on off on off off off off on off off off on off off on off on off off off on on off on off on off off on off off off on off off off on off off off off on off off off on on on off on on off off on off on on on off on on off on on on off off off off off on on off off on off off off off off on off off on on off on on off on off off off on off off off off on on off on off off on off off on off on off off off off off off off off on on off on off off off.args with
* Add def args = task.ext.args line to all modules in script section
* Replace options.args with args and args_list
* Initialise args2 and args3 properly
* Replace container syntax
* Revert container changes for cellranger/mkref
* Replace getProcessName in all modules
* Replace getSoftwareName in all modules
* Unify modules using VERSION variable
* Replae options.suffix with task.ext.suffix
* Remove NF version restriction for CI
* Bump NF version in README
* Replace task.process.tokenize logic with task.process
* Minor tweaks to unify syntax in tests main.nf
* Add a separate nextflow.config for each module
* Transfer remaining module options to nextflow.config
* Remove addParams from tests main.nf
* Remove TODO statements
* Use -c to import module specific config
* Bump NF version to 21.10.3
* Fix tests for artic/minion
* Fix broken publishDir syntax
* Standardise and fix obvious failing module tests
* Remove kronatools to krona
* Comment out tags in subworkflow test.yml
* Fix failing module tests
* Add consistent indentation to nextflow.config
* Comment out subworklow definitions
* Fix kallistobustools/ref
* Fix rmarkdownnotebook
* Fix jupyternotebook
* Quote task.process
* Add plink2/vcf to pytest_modules.yml
* Remove NF_CORE_MODULES_TEST from pytest CI
* Fix more tests
* Move bacteroides_fragilis to prokaryotes folder
* Fix cooler merge tests
* Fix kallistobustools/count tests
* Fix kallistobustools/ref tests
* Update test_10x_1_fastq_gz file for kallistobustools/count tests
* Fix bcftools/query tests
* Fix delly/call tests
* Fix cooler/zoomify tests
* Fix csvtk/split tests
* Fix gatk4/intervallisttools tests
* Fix gatk4/variantfiltration
* Fix pydamage/filter tests
* Fix test data for unicycler
* Fix gstama/collapse module
* Fix leehom tests
* Fix metaphlan3 tests
* Fix pairtools/select tests
* Update nextflow.config
* Update nextflow.config
* feat: update syntax
* Fix arriba tests
* Fix more failing tests
* Update test syntax
* Remove comments from tests nextflow.config
* Apply suggestions from code review
* Fix kallistobustools/count module
* Update dumpsoftwareversions module
* Update custom/dumpsoftwareversions
* Add args2 to untar module
* Update leftover modules
* Remove last remaining addParams
* Change syntax from task.ext.suffix to tast.ext.prefix
* Change nextflow.config in all tests to use ext.prefix instead of ext.suffix
Co-authored-by: JoseEspinosa <kadomu@gmail.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: MaxUlysse <max.u.garcia@gmail.com>
* Add comment line for consistency
* Remove all functions.nf
* Remove include functions.nf and publishDir options
* Replace options.args3 with task.ext.args3 - 3 modules
* Replace options.args3 with task.ext.args3 - 17 modules
* Replace {task.cpus} with task.cpus
* Replace off on off off off off off off off on off on off on off off off on off off off on on off off off on on off off off off off off off on off off off off on off on on off off off on on on on off off off on off on on off on on off off on on on off on on off on off off off off on off off off on off off on off on off off off on on off on off on off off on off off off on off off off on off off off off on off off off on on on off on on off off on off on on on off on on off on on on off off off off off on on off off on off off off off off on off off on on off on on off on off off off on off off off off on on off on off off on off off on off on off off off off off off off off on on off on off off off.args with
* Add def args = task.ext.args line to all modules in script section
* Replace options.args with args and args_list
* Initialise args2 and args3 properly
* Replace container syntax
* Revert container changes for cellranger/mkref
* Replace getProcessName in all modules
* Replace getSoftwareName in all modules
* Unify modules using VERSION variable
* Replae options.suffix with task.ext.suffix
* Remove NF version restriction for CI
* Bump NF version in README
* Replace task.process.tokenize logic with task.process
* Minor tweaks to unify syntax in tests main.nf
* Add a separate nextflow.config for each module
* Transfer remaining module options to nextflow.config
* Remove addParams from tests main.nf
* Remove TODO statements
* Use -c to import module specific config
* Bump NF version to 21.10.3
* Fix tests for artic/minion
* Fix broken publishDir syntax
* Standardise and fix obvious failing module tests
* Remove kronatools to krona
* Comment out tags in subworkflow test.yml
* Fix failing module tests
* Add consistent indentation to nextflow.config
* Comment out subworklow definitions
* Fix kallistobustools/ref
* Fix rmarkdownnotebook
* Fix jupyternotebook
* Quote task.process
* Add plink2/vcf to pytest_modules.yml
* Remove NF_CORE_MODULES_TEST from pytest CI
* Fix more tests
* Move bacteroides_fragilis to prokaryotes folder
* Fix cooler merge tests
* Fix kallistobustools/count tests
* Fix kallistobustools/ref tests
* Update test_10x_1_fastq_gz file for kallistobustools/count tests
* Fix bcftools/query tests
* Fix delly/call tests
* Fix cooler/zoomify tests
* Fix csvtk/split tests
* Fix gatk4/intervallisttools tests
* Fix gatk4/variantfiltration
* Fix pydamage/filter tests
* Fix test data for unicycler
* Fix gstama/collapse module
* Fix leehom tests
* Fix metaphlan3 tests
* Fix pairtools/select tests
* Update nextflow.config
* Update nextflow.config
* feat: update syntax
* Fix arriba tests
* Fix more failing tests
* Update test syntax
* Remove comments from tests nextflow.config
* Apply suggestions from code review
* Fix kallistobustools/count module
* Update dumpsoftwareversions module
* Update custom/dumpsoftwareversions
* Add args2 to untar module
* Update leftover modules
* Remove last remaining addParams
Co-authored-by: JoseEspinosa <kadomu@gmail.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: MaxUlysse <max.u.garcia@gmail.com>
* Make targets.bed optional when running in wgs mode
* added test for cram
* Update test_data_config with new reference.cnn
* Update main.nf to allow tumor-only running
Still need a unit-test for this. Almost ready, but needs this file as input https://github.com/nf-core/test-datasets/blob/modules/data/generic/cnn/reference.cnn
* re-writing previous changes, but now it wont crash the entire CI-setup
* fixing overlooked merge conflict
* last overlooked merge-conflict
* move all files to batch subfolder
* adding an optional input for a reference file (needed when running germline and tumoronly)
* minor typo
* update meta.yml
* aligning code, renaming cnvkit to cnvkit_batch, renaming tumorbam to tumor, normalbam to normal
* Update pytest_modules.yml
Co-authored-by: EC2 Default User <ec2-user@ip-172-31-21-198.us-west-2.compute.internal>
Co-authored-by: Lasse Folkersen <lassefolkersen@gmail.com>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Fix picard/markduplicates with new options syntax
* Delete md5sum for bam files and add contains for metrics.txt
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
* Added vcf_index to vcf tuple; output to vcf.gz format.
* Fix: extra new line in meta.yml.
* addressed review feedback
* fix: editorconfig error
* fix: gatk memory flag
* fix: editorconfig error
* fix: Indentation
fix: Indentation
* Fix: lint editorconfig error
Removed one extra space
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
* initial commit to setup branch
* workflow finished
* Update nextflow.config
* tumour to tumor, getpileup passed as nomral and tumor
* paired_somatic renamed to tumor_normal_somatic
* Apply suggestions from code review
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* Update subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/main.nf
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* updated index names in meta.yml
* changed index file names in main script and test
* Apply suggestions from code review
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* Apply suggestions from code review
* fixed bug from changes
* Apply suggestions from code review
* tests should now work after the yml update
* Update pytest_modules.yml
Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
* initial commit to set up new branch
* save changes to checkout
* workflow working, still needs test.yml and meta.yml, also fix versions file
* subworkflow finished
* Update pytest_subworkflows.yml
* Update pytest_subworkflows.yml
* Update pytest_subworkflows.yml
* fix config subworkflow name
* Update main.nf
* Update pytest_subworkflows.yml
* fixed md5sum issue likely caused by gatk version update
* tumour changed to tumor
* old dir deleted
* Comments added to explain use of placeholders '[]'
* updated index names, input channel renamed to input
* Apply suggestions from code review
* updated to perform new subworkflow testing
Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* fasta_fai_dict tuple is now split into separate input channels
* fix: lint errors
* fix: pytest errors
* Update modules/gatk4/splitncigarreads/meta.yml
* Update modules/gatk4/splitncigarreads/main.nf
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* add new nucmer module
* Apply suggestions from code review
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
* update tests with file produced by input
* Update main.nf
* Update meta.yml
Co-authored-by: Michael Cipriano <mcipriano@gmail.com>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* ci: Remove pytest_subworkflows
* ci(bam_sort_samtools): Depend on paths-filter instead of pytest-workflow
Co-authored-by: Harshil Patel <drpatelhh@gmail.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
* ci: Revert back to one job branch
* ci(align_bowtie2): Run tests that depend on bam_sort_samtools
* ci: Fix anchor not being created yet
* ci: Update sra_fastq tags and pytest_modules
* fix(bam_sort_samtools): Update nextflow.config with params
* test(subworkflows): Update gatk_create_som_pon tags
* ci: Point to subworkflow_hacks branch of nf-core tools
Co-authored-by: Harshil Patel <drpatelhh@gmail.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
* created and initialised krona module
* Added kronatools/ktimporttaxonomy module
* removing previous redundant work
* added contains info for html
* edited contains in test.yml
* Update get versions
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
* remove old syntax
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
* rewording module description
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
* added detailed keywords
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
* update syntax and tool version
* fixed meta.yml issues
* remove contains line from test.yml
* re-wrote module after nf-core/tools update - should work now
* removed md5
* Update modules/kronatools/ktimporttaxonomy/main.nf
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
* update meta save
* removed typo
* double quotes to single quotes around html
* re-ran test, which updated md5
* removed md5
* 'classifier' removed to fix linting
* update version
* removed erroneous ktimporttaxonomy2
* Updated input to include meta and database
* fixed tab issues in yaml
* added `contains` to test.yml
* edited `contains` in test.yml
* trying another `contains`
* retrying `contains`
* contains with extra line
* removed classifier from tag
* Apply suggestions from code review
* Update meta.yml
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Add tests and yml file for macs2/callpeak
* add format option for macs2
* update macs2/callpeak to accept format argument
* update test.yml
* update the container version.
* try to fix the issue in conda container.
* Update conda and containers
* Going back to previous container versions
Co-authored-by: JoseEspinosa <kadomu@gmail.com>
* add software/cooler
* fix the wrong files uploaded.
* create a branch for cooler/zoomify
* Apply suggestions from code review
* update functions.nf to new version.
* update the test file to test-datasets.
* update the test method of zoomify
* update dump test file.
* update version.txt to version.yml
* Update modules/cooler/dump/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* fix the output bug of versions update to pytest_modules.yml
* update the test file path and fix the output versions.
* Update modules/cooler/dump/main.nf
* indent
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
* New modules added: issues #200 and #310
* Update main.nf
* Update meta.yml
* Update tests/modules/gatk4/genotypegvcfs/main.nf
* Apply suggestions from code review
* Update main.nf
* Updating tests for GenomicsDB input and adding the path for this test resource to test_data.config
* Some minor changes on one of the test files I forgot to include
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: GCJMackenzie <43276267+GCJMackenzie@users.noreply.github.com>
* add software/cooler
* fix the wrong files uploaded.
* create a branch for cooler/merge
* remove the bin_size from metadata.
* update the test_data to test-datasets
* update pytest_modules.yml
* update the test file from single input file to two input file.
update the output file from hdf5 to bedpe.
* update the version.txt to version.yml and functions.nf
* change version.yml to versions
* update the test file path and fix the output versions.
* Update meta.yml
Correct "version" to "versions"
* Update main.nf
Fix typo
* Update main.nf
Remove some spaces
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
* commit but won't be used because pmdtools should have a submodule
* added submodule pmdtools/filter
* removed pmdtools module created before deciding to design two submodules
* oops forgot to remove a TODO
* removed white space meta.yml, removed v in version and manually added submodule /filter to test
* Update pytest_modules.yml
* Update main.nf
added split_cpus for multi-tools module resources
* Update test.yml
added .pmd extension to match modules/ main.nf
* Update test.yml
update md5sum
* Update singularity and docker build in main.nf
From build 4 to 5 in order to match the conda one
* Update modules/pmdtools/filter/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/pmdtools/filter/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/pmdtools/filter/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/pmdtools/filter/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/pmdtools/filter/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/pmdtools/filter/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/pmdtools/filter/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/pmdtools/filter/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/pmdtools/filter/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update main.nf adding samtools version
we need both pmdtools and samtools versions
* Update main.nf remove .pmd extension
* Update test.yml md5sum
Because file extension changed
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* feat: update gatk4 from 4.2.0.0 to 4.2.3.0
* update md5checksum
* commit all files
* actually checksum was good, but I suspect something fishy with the tests
* added template
* integrated module
* added fasta index info
* test works, have placeholder data for baits until test-data PR is merged
* added new files to config
* updated test files
* fixing fails ✨
* okay final fix here on the md5sum :face_palm:
* md5sum variable
* update meta.yml to reflect consistency to main.nf
* reverted version so conda works
* Apply suggestions from code review
Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
* md5sum can't be generated consistently for output
Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
* add pydamage module
* remove TODOs
* split module by subcommands
* update version parsing
* remove forgotten TODOs
* update module names
* remove old holistic module
* Update modules/pydamage/analyze/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* add keywords
* update resource requirement
* Update modules/pydamage/filter/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/pydamage/filter/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* merge from upstream
* update pydamage from upstream
* add freebayes
* update pydamage test from upstream
* fix meta.yml
* update functions.nf
* update test.yml
* update version parsing
* update version parsing
* fix indentation
* Update modules/freebayes/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/freebayes/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/freebayes/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* add optional inputs
* Update modules/freebayes/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* add bed test
* add metabat2 module
* only freebayes
* remove metabat2
* update md5sum because of vcf including date of the day
* add keyword
* rescue conflicted files
* attempt to fix ECLint
* add pytest workflow for metabat
* remove -
* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/metabat2/metabat2/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/metabat2/metabat2/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* add optional inputs/outpus
* remove trailing whitespace
* first cmseq commit
* compressing and removing not reproducible md5sums
* save intermediate work
* follow symlinks while decompressing
* add cmseq/polymut
* add polymut
* add extra test with optional input file
* remove metabat2
* Update modules/cmseq/polymut/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/cmseq/polymut/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/cmseq/polymut/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* fix file extension
* Update modules/cmseq/polymut/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* add test without bam index
* split tests in workflows
* answer PR review
* report version from variable
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Implement PLINK_EXTRACT module
* fix plink version number
* Update main.nf
* Update test_data.config
* Update modules/plink/extract/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* just use one channel
* fix test with new channel input
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* commiting changes to switch branch
* commit to setup remote branch
* first draft of the sompon workflow
* keep branch in line with gendb bugfixing
* Update test.yml
* tidy up main.nf
* fixed md5sum
Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
* saving changes to checkout
* saving to sort out other branch
* removed yml tracking of files that cant be tracked due to directory name changing between runs
* test data added, ready for pr
* fix eol linting error
* Update modules/gatk4/genomicsdbimport/main.nf
Co-authored-by: Francesco L <53608000+lescai@users.noreply.github.com>
* merging with master
* update push to show progress
* tests now working untar able to pass data to genomicsdbimport
* commit to checkout
* tests updated, module reworked to simplify and emit updated gendb
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* update meta.yml
Priority of input options changed, updated to reflect this
* Update test.yml
name prefix changed in main script, test.yml updated to reflect this
* fix tests due to review changes
* bug fixes, multicalling samples and gendb emissions now fixed
* Update pytest_modules.yml
* Update meta.yml
Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Francesco L <53608000+lescai@users.noreply.github.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
* first commit with imputeme as a module. Extensive re-write of imputeme-code, resulting in release v1.0.7 that is runnable in the next-flow framework.
Co-authored-by: EC2 Default User <ec2-user@ip-172-31-21-198.us-west-2.compute.internal>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Pontus Freyhult <pontus_github@soua.net>
* add base code from samblaster
* added test yml
* fixing versions files, should this be the cause of online lint failures
* removed tmp files that shouldn't be there
* fixing output file name - 1
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* fixing output file name - 2
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* fixing output file name - 3
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* fixing output file name - 4
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* fixing output file name - 5
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* fixing output file name - 6
* fixed indent
* fixed input name and updated test.yml file with new name
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Specify more guidelines on input channels
* Linting
* Updates based on code review
* Update README.md
* Fix broken sentence
* feat: add megahit module, currently decompressed output
* Update main.nf
* Update tests/modules/megahit/test.yml
Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* feat: compress all outputs, remove md5sums due to gz stochasicity
* fix: wrong conda channel for pigz
* fix: broken singleend tests and update meta.yml
* Missed one
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* fix: pigz formatting
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Apply suggestions from code review
* Add GUNC download_db and run commands
* Bump with version without zgrep
* Apply suggestions from code review
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
* Harshil formatting
* Apply suggestions from code review
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
* Add CRAM support to allelecounter
* Update meta.yml
* Rename bam,bai to input,input_index
* Apply suggestions from code review
* Fix reference to renamed variable
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* readcounter module for hmmcopy
* Changed version number
* Fix indentation
* Update main.nf
* Update modules/hmmcopy/readcounter/main.nf
Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk>
Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
* hmmcopy gccounter working
* Update modules/hmmcopy/gccounter/main.nf
Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
* Update main.nf
Changed version to 0.1.1 as the container says
Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk>
Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
* files created for createsompon, script written, meta written, still needs tests
* updated to 2.0.0 method input, however this requires a genomicsDB input now
* script finished, meta yaml updated. Tests working locally, test yaml made, needs genomicsdb example on nf-core to run repository tests
* versions updated, issue with test data not able to download directory
* updated tests to include repo-side data
* Apply suggestions from code review
* Update modules/gatk4/createsomaticpanelofnormals/main.nf
* temp commit to allow checkout
* updated createsompon tests to use tarred gendb
* resolve conflict
* Update tests/modules/gatk4/createsomaticpanelofnormals/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* saving changes to checkout
* saving to sort out other branch
* removed yml tracking of files that cant be tracked due to directory name changing between runs
* test data added, ready for pr
* fix eol linting error
* Update modules/gatk4/genomicsdbimport/main.nf
Co-authored-by: Francesco L <53608000+lescai@users.noreply.github.com>
* merging with master
* update push to show progress
* tests now working untar able to pass data to genomicsdbimport
* commit to checkout
* tests updated, module reworked to simplify and emit updated gendb
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* update meta.yml
Priority of input options changed, updated to reflect this
* Update test.yml
name prefix changed in main script, test.yml updated to reflect this
* fix tests due to review changes
Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Francesco L <53608000+lescai@users.noreply.github.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* add new module samtools_depth
* fixed main.nf for samtools/depth
* add new module mtnucratio
* fix main.nf
* Apply suggestions from code review
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Apply suggestions from code review
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* layout in main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* hifiasm copied from fastqc
* hifiasm tests init from fastqc
* meta.yml init; test.yml and main.nf for printing version
* Add hifiasm version printing
* Removed spaced on an empty line
* Reverted hifiasm from main
* Added extension input for bedtools sort
* whitespace
* Updated docs
Co-authored-by: Sviatoslav Sidorov <sviatoslav.sidorov@crick.ac.uk>
Co-authored-by: Svyatoslav Sidorov <svet.sidorov@gmail.com>
* adding template for module groupreadsbyumi
* update modules with code
* strategy is required argument so moving it to input rather than options.args
* tests successful committing yml
* added meta to output
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
* Templates for new module
* pe only test passing
* only_pe and only_se passing
* only_pe, only_se, mixed passes
* Multiple pe + se tc passes
* Passing args works
* Add 'interleaved' to description
* Fixed linting message
* Update modules/khmer/normalizebymedian/main.nf
Good point.
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
* Update meta.yml
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
* Make samtools/merge cram compliant
* samtools/stats cram compliance
* update yml file
* samtools/view to deal with crams
* Update tests to make sure cram works
* also fix tmp dir and min mem in one go
* basequalityrecal test for cram + min mem + tmpdir
* update haplotypecaller for sarek
* update haplotype yml
* update markdup to allow multiple bams, take out params to be passed with options.args
* remove TODO statement
* Remove variable md5sum
* add emtpy input to stats module in subworkflows
* subworkflows seem to work now on my side
* Apply code review
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* replace bam with input to be more inclusive
* rename everywhere
* rename input
* remove variable checksum
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* new mitochondria mode added, tests updated to allow for temp fix for test data
* add cram test
* bam/bam_idx renamed to input and input_index
Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
* added template for module
* update main
* added specific code
* wrong variable name in else script
* added tests for both split and nosplit
* docker test successful - updating yaml
* adding echo to version print
* add new assembly scan module
* add newline endings
* fix newline ending
* add newline at end
Co-authored-by: Peri <rrx8@cdc.gov>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
* First step into creating a seqtk/mergepe module to interleave fastQ input
* First rewrite of main.nf to make the module perform the desired (interleave/merge of pe reads) task
* Modifications to test the new seqtk/mergepe module.
* Improving the seqtk/mergepe module to output single end reads as well, and making sure tests work
* Modified so that gzip uses -n and that single read entries are symlinked with ln -s instead of copied, therefore updated test.yml as well.
* Fix trailing whitespaces
Co-authored-by: Daniel Lundin <daniel.lundin@lnu.se>
* Provide an exisiting bam file for optitype
* Update main.nf
Attempt at fixing this with new testing data
* Trying slightly different approach
* Mini fixes, not sure whats wrong here
* Add bam file with NM tags in all reads for optitype
Co-authored-by: Alexander Peltzer <apeltzer@users.noreply.github.com>
Co-authored-by: Alexander Peltzer <alexander.peltzer@boehringer-ingelheim.com>
* add module main porechop
* update porechop main
* add porechop functions
* update meta porechop
* add test main porechop
* add porechop pytest yml
* add porechop test.yml
* Update modules/porechop/meta.yml
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
* re-add porechop avoid conflict
* Update modules/porechop/meta.yml
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
* fix prefix suffix
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
* add new module samtools_depth
* fixed main.nf for samtools/depth
* Apply suggestions from code review
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* added template for fastqtobam
* porting old code into new template
* update with missing getprocessname function
* test completed - updating all
* fixed linting issues
* improved reading
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
* 👌 IMPROVE: Add some pacbio test files
* 🐛 FIX: Add Pacbio index to test_data.config
* 👌 IMPROVE: Re add 10000 data test
* 👌 IMPROVE: Add some pbindex
* 🐛 FIX: Add pbi extension to files
* 📦 NEW: Add galgal6 chr30 test data
* 📦 NEW: Add bamtools module
* 👌 IMPROVE: Ignore test data
* 👌 IMPROVE: Update to last templates version
* 👌 IMPROVE: Update module to last template version
* 👌 IMPROVE: Update module to last template version
* 👌 IMPROVE: Final version of test datasets config
* 👌 IMPROVE: Remove useless index + Fix Typos
* 👌 IMPROVE: Add some pacbio test files
* 🐛 FIX: Add Pacbio index to test_data.config
* 👌 IMPROVE: Re add 10000 data test
* 👌 IMPROVE: Add some pbindex
* 🐛 FIX: Add pbi extension to files
* 📦 NEW: Add galgal6 chr30 test data
* 📦 NEW: Add bamtools module
* 👌 IMPROVE: Ignore test data
* 👌 IMPROVE: Update to last templates version
* 👌 IMPROVE: Update module to last template version
* 👌 IMPROVE: Update module to last template version
* 👌 IMPROVE: Final version of test datasets config
* 👌 IMPROVE: Remove useless index + Fix Typos
* 👌 IMPROVE: Update with new versions.yml file
* 🐛 FIX: Update meta.yml + correct typos
* Update modules/bamtools/split/meta.yml
Add bam, split, chunk tags
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* 🐛 FIX: Correct meta.yml
* 🐛 FIX: Grab software name using ${getSoftwareName(task.process)}
* 🐛 FIX: Update test.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* files created for createsompon, script written, meta written, still needs tests
* updated to 2.0.0 method input, however this requires a genomicsDB input now
* script finished, meta yaml updated. Tests working locally, test yaml made, needs genomicsdb example on nf-core to run repository tests
* versions updated, issue with test data not able to download directory
* updated tests to include repo-side data
* Apply suggestions from code review
* Update modules/gatk4/createsomaticpanelofnormals/main.nf
Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* add liftOver module
* add liftover module tests
* fix getProcessName
* fix tests
* fix out of date function
* version numbers should be numeric
* drop versions.yml from test.yml
* Update modules/ucsc/liftover/main.nf
Remove software name variable
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
* Update tests/modules/ucsc/liftover/main.nf
Use test chain file
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
* add genome_chain_gz to test data config
* update md5sum for new chain test data
* Fix indentation in file declaration
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
* hifiasm copied from fastqc
* hifiasm tests init from fastqc
* meta.yml init; test.yml and main.nf for printing version
* Add hifiasm version printing
* Removed spaced on an empty line
* Reverted hifiasm from main
* Updated seacr callpeak to include a control threshold
* Whitespace
Co-authored-by: Sviatoslav Sidorov <sviatoslav.sidorov@crick.ac.uk>
Co-authored-by: Svyatoslav Sidorov <svet.sidorov@gmail.com>
* Reduce number of required input files for damage profiler
* Remove rebugging
* Add optional species list file.
* Working pending updated test-dataset update
* Add genome header to config
